I just bought my first FZR400.
A 1990 US model 1WG with the deltabox swingarm and twin pot calipers.

First issue is about cooling. It get's hot... like, it gets really hot if I'm traveling at anything under 35mph. It doesn't boil over.
I intend to swap in an FZR600 radiator and an auxiliary fan switch to get slightly better cooling, but I need to know what all I'll need. I know I'll need to make some lower brackets for the core, but do I need the 600 coolant lines as well?

The other issue is a matter of swapping on a 17" rear wheel.
Breathe a sigh of relief; I don't need the list of options. I already have a 3TJ swingarm and wheel.
Is there anything special I need to do to fit this swinger into the 1WG frame?
I have a GSXR 600 shock, so do I need to get different dogbones? If so, how long?
I know the sprockets aren't going to line up, so what drive sprocket should I swap in?
Rear brake caliper is super frozen. What are my replacement options?

Last issue is it hates coming off idle. I have to blip the throttle 2-3 times to get the revs up so I can take off from a stop, otherwise the engine will bog down and die. Less of a problem as the bike gets hot, but comes back if I turn off the bike to go into the shops or fill it with petrol. Jetting? Balancing?

Any help would be greatly appreciated. This is easily the best handling bike I've ever owned, and I want to cool this beast down and roll on some modern rubber.

If you have a new to you fzr, I would - service it so first up I'd check the valve tolerances, the inlet valves close up and it can affect the starting and running. Next, because you've done the valves clean the carbs and balance them - if the bike still isn't running very well get a dyno tune. Obviously the usual sevice items will help, new plugs, oil filters ... there's a KnN that should fit the airbox it won't add anything to performance but at least you can clean it. Drop the sump on the oilchange (just this once) and clean the sludge out with petrol.
Cooling. Most Yamahas get hot, like really hot, until the thermostat opens and you get some cool air. All new owners worry about it but they don't boil and the only way you know is by the temp gauge (maybe it's the gauges they use ????) anyway during your service you'll be taking the radiator off ... it helps with access to the plugs. Make sure there isn't a load of crap stuck in there and have a look at the fins, carefully bend them back. Personally I prefer not to fit a fan switch because then you need to turn it on / off. Using some new coolant / distilled water might well improve things, make sure you have a bit in the expansion chamber in the tail of the bike. Take a picture of the hose connections by the rad cap - don't get them the wrong way up.

I haven't done either of the two swaps - do a search and see if there's any more info on this forum. Maybe contact Kayla from Projection Components, they make a few things for FZRs which might help. They do a pair of 4 way adjustable dog bones which might help with the shock swap - put the bike on a paddock stand or wheel chock so it's vertical. make a T section from some wood and put some masking tap on the bike's tail. Mark the height on the bike and the wood fit up the shock and repeat then use the dogbones to adjust the ride height. Don't be tempted to jack the bike up too high at the back.

The bike has 254 miles on a fresh rebuild from a very reputable shop in San Francisco, so I doubt it needs to be serviced. After I finish breaking it in, I'll change oil and check valves. I am going to check the carbs though, because the idle (while smooth and consistent at 1100 rpm) sounds a little lumpy.
I just want to get some better cooling in there because this thing gets hot like my Ducati, and HATES rolling slow in traffic... which I have to deal with a lot in the Bay Area., which is why I'd like to also have a fan switch.

The swingarm swap has been hard to find info on. I've seen that people have done it, but nobody explains the process. Does it just bolt in?

Once I get the arm installed, I'll deal with the suspension linkage (I was hoping that someone would have a suggestion) and I only plan on raising the rear a couple centimeters.

I seem to remember the swingarm pivot might be a smaller dia and the arm might be wider but i dont know so dont take it as gospel. Would the 3tj rear fit in your arm ? I thought they used a 3en2 arm and they aparently had two widths.
The 160 profile tyre is matched with a 120 front which uses a 3.5" wheel the Foxeye 600 is the closest (same as the 3tj) but i think the spindle is a larger dia

I can handle machining spacers and collars if I need them.
Not sure that my 3en2 swingarm will work because it uses the same 18" wheel as the old 1WG swingarm.
For the front, if I need a 120; could I just swap on a YZF600 front end? First gen R6? I already have my bars under the top clamp, so it wouldn't matter to me if the other forks are a little shorter.

I've had overheating issues with a couple of 1WGs in the past. Funnily enough removing the lower fairings lowered the running temp dramatically. However on my latest 1WG (track bike with fairing lowers still on) I fitted a FZR600 rad. It is about 20% larger length x width and it does seem to run a lot cooler now. It mounts right up to the 400 mounting points although I had to put a couple of wider spacers in each side.
By the way the 600 fan is different from the 400 fan (different length mounting arms). I didn't bother fitting a fan with the 600 rad figuring it would run cooler and not need it.
Finally the hoses route differently top and bottom. You could either get the top & bottom hoses from the 600 or make something up. I had some silicone hose bends lying around so I was able to use those along with the stock 400 hoses cut up to make it work.
Hope this helps.